R/hcr_set_recErrors.R

In einarhjorleifsson/mac: Miscalaneous set of functions related fish stock assessment work

#' @title HCR: Setup of recruitment error structure
#' 
#' @description This function is modified from the original in the fishvise package.
#' In that package there was only one parameter estimate (a, b and cv). Here we have 
#' different parameters for each iteration, and even different recruitment model.
#' 
#' @export
#' 
#' @param d XXX
#' @param ctr XXX
#' 
hcr_set_recErrors <- function(d,ctr) 
{
  
  n_years  <- dim(d)[1]
  n_hrates <- dim(d)[2]
  n_iters  <- dim(d)[3]
  
  # Recruitment: cv & autocorrelation
  x <- array(rnorm(n_years * n_iters),
             dim=c(n_years , n_iters))
  
  for (y in 2:n_years) x[y,] <- ctr$r_rho * x[y-1,] + sqrt(1 - ctr$r_rho^2) * x[y,]
  
  x <- exp(x*ctr$ssb_pars$cv)
  for (h in 1:n_hrates) d[,h,] <- x
  
  return(d)
}